[Bioc-devel] pandoc SSL error on malbec2 and tokay2

Martin Morgan martin.morgan at roswellpark.org
Wed Sep 6 20:48:18 CEST 2017

On 09/05/2017 10:35 AM, Nan Xiao wrote:
> Hey Kasper,
> - I really appreciate your help. Although it didn't help answer the
>    question directly, I think it would still be necessary to clarify
>    some facts:
> 1. I agree that using "non-standard fonts" could bring better aesthetics
>     for a particular group of people -- maybe not everyone. But the
>     "occasional" build problem should not be a reason why this
>     personalization is discouraged. In fact, such build problem should
>     not happen a lot (or, at all). I have been using such non-standard
>     fonts for my 9 regularly updated R packages on CRAN since 2015, and I
>     didn't encounter a single vignette build issue.
> 2. I've used BioCStyle since 2014, but eventually decided to switch to
>     my own style years later because of the frequent build errors it
>     caused back then. Maybe that's only my personal, limited experience
>     (and I've seen the recent BioCStyle v2 got a lot of improvements),
>     but this is the main reason why I trust the document style
>     controllable by myself more than the other options.

It's great that CRAN is so efficient and robust; I really don't know how 
they do it.

I'll re-iterate with Kasper that these customizations cost us 
(Bioconductor core team) time -- maybe your package fails only once 
every 1000 days, but there are a thousand developers so...

Fixing BiocStyle once fixes it for all developers, while fixing a custom 
issue once fixes it for just one developer.

And users can choose to build vignettes, so they'll have to 
trouble-shoot whatever issues are unique to your package.

There really is value all around in keeping things simple.

As for your particular issue, it seemed to fail on 3 of the 5 builds 
that have reported yesterday, 2 of the five today. Have you noticed this 
for several days in a row?

I did ask about pandoc on the builders; they have

   malbec1/2 are at version 1.19.1
   tokay1/2 have 1.17.2
   veracruz1/2 have 1.19.2.

of course we try to keep these in sync, but also do not go to 
extraordinary lengths to install the same version across platforms. 
These have not changed in the time frame that would cause your builds to 
experience recent failures.

This seems very much like a transient Internet access issue. Transient 
access is one of the most difficult to debug, especially on our 'build' 
servers where the loads experienced by the machines can vary a lot, and 
where the vagaries of Internet connections can be catastrophic for a 
build but almost unobserved by an individual investigating the problem.


> Best,
> -Nan
> --
> https://nanx.me
> On Tue, Sep 5, 2017, at 09:16, Kasper Daniel Hansen wrote:
>> Build errors like these (related to processing of vignettes) happens
>> occasionally.  I _strongly_ suggests not not using non-standard fonts
>> or advanced layout features.  The small advantage of this (better
>> aesthetics according to the package writer, but not always according
>> to everyone who reads it) does not outweigh the disadvantage of
>> package failure and associated time burden on the package authors and
>> the build system / admins.  I strongly suggests using BiocStyle; I
>> know that the layout doesn't agree with everyone, but (1) you can
>> expect that the build system will support this and (2) aesthetics is
>> highly personal anyway.>
>> Best,
>> Kasper
>> On Mon, Sep 4, 2017 at 12:38 PM, Nan Xiao <me at nanx.me> wrote:
>>> Dear BioC,
>>>   - I see some very recent build errors for my packages (vignettes)
>>>     which>>  use Google Fonts:
>>>   pandoc: Could not fetch
>>> https://fonts.googleapis.com/css?family=Alegreya+Sans:400,400i,700
>>>   TlsExceptionHostPort (HandshakeFailed Error_EOF)
>>>   "fonts.googleapis.com">>  443
>>>   For example
>>> https://bioconductor.org/checkResults/release/bioc-LATEST/Rcpi/malbec2-buildsrc.html>>
>>>   There were no such issues building these vignettes before, and
>>>   I'm not>>  even sure if this is a new issue caused by Google or pandoc.
>>>   Could you>>  please shine some light on this?
>>>   Thank you,
>>>   -Nan
>>>   --
>>> https://nanx.me
>>>   _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 	[[alternative HTML version deleted]]
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